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>> Problem is that the index and TOC didn't regenerate -
sections that were deleted etc still appeared in both. <<
Since these are generated files, don't even mess with
them, as you found, just delete and re-generate them.
You are right, they are getting tripped up by the old
files and their previous location.
It's not worth the hassle to do anything by re-generate
the files. If this doesn't work, create a new book and
add the files to the new book. This will clear out any
links to the old files.
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